The use of next generation sequencing for improving food safety: Translation into practice.

Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use.

Impact of soymilk consumption on 2,4-dinitrofluorobenzene-induced contact hypersensitivity and gut microbiota in mice.

Soymilk is rich in phytochemicals such as soy isoflavones (SIs) and soyasaponins (SSs). Dietary SIs and SSs display inhibitory effects on contact hypersensitivity (CHS), which was reported in a mouse model for allergic contact dermatitis (ACD); however, the beneficial effects of soymilk consumption on CHS remain unknown. Here, we studied the effects of drinking soymilk on CHS and gut microbiota. Soymilk consumption attenuated ear oedema and swelling, decreased the infiltration of Gr-1-positive cells into ear tissues, and reduced the production of chemokine (C-X-C motif) ligand 2 and triggering receptor expressed on myeloid cells-1 in ear tissues. The analysis of bacterial 16S ribosomal RNA gene sequences indicated that CHS caused changes in the gut microbiota structure and that consuming soymilk reduced these changes. These results suggest that soymilk consumption may be of therapeutic value for patients with ACD and may help control the balance of intestinal microbiota.

Inhibitory effects of dietary soy isoflavone and gut microbiota on contact hypersensitivity in mice.

Soy isoflavones (SIs) are abundant in soybeans and have inhibitory effects on contact hypersensitivity (CHS), which is often used as a mouse model for allergic contact dermatitis (ACD); however, their therapeutic mechanisms remain unknown. We studied the suppressive activity of dietary SI and gut microbiota on dinitrofluorobenzene (DNFB)-induced CHS. Low-dose SI diets alleviated DNFB-induced ear swelling and oedema and decreased infiltration of Gr-1-positive cells into ear tissue. In addition, dietary SIs also decreased interleukin-1ß and chemokine (C-X-C motif) ligand 1 production in ear tissue compared to controls. Furthermore, ciprofloxacin and metronidazole treatments blocked the suppressive activity of dietary SIs on CHS, whereas vancomycin treatment had a marginal effect. These antibiotic treatments differed in their effects on the gut microbiota composition. These results demonstrated that consumption of physiologically relevant doses of SIs reduced CHS symptoms, and suggested that the gut microbiota influenced their suppressive activities on CHS.

Inhibitory effects of dietary soyasaponin on 2,4-dinitrofluorobenzene-induced contact hypersensitivity in mice.

Soyasaponins (SSs) abundant in soybean have anti-inflammatory activities; however, their therapeutic effects on allergic contact dermatitis (ACD) remain unknown. To assess the effects of SS-enriched diets on ACD, we used a mouse model of contact hypersensitivity (CHS). Mice were fed low-dose or high-dose SS-containing diets for 3 weeks prior to CHS induction with 2,4-dinitrofluorobenzene (DNFB). The low-dose SS diet attenuated DNFB-induced ear swelling and tissue oedema, and reduced the number of infiltrating Gr-1-positive myeloid cells. Low-dose, but not high-dose, SSs decreased chemokine (C-X-C motif) ligand 2 (CXCL2) and triggering receptor expressed on myeloid cells (TREM)-1 production in ear tissues, compared to a control. Taxonomic 16S rRNA analysis revealed significant alterations in faecal microbiota caused by CHS, which were reversed by low-dose SSs. The low-dose SS and non-CHS groups clustered together, while the high-dose SS group split between CHS and non-CHS clusters. Our results demonstrated that low-dose SSs alleviated CHS symptoms by attenuating inflammation and improving the intestinal microbiota composition, suggesting that dietary SSs may have beneficial effects on ACD.